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update examples to match others

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This commit is contained in:
Axel Kohlmeyer
2022-10-18 14:48:37 -04:00
parent b4a65a1932
commit 38c24b68ad
7 changed files with 473 additions and 198 deletions
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26
examples/ASPHERE/flat_membrane/in_flat_membrane → examples/ASPHERE/flat_membrane/in.flat_membrane
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@ -1,4 +1,4 @@
# flat membrane demo
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d2 equal sqrt(3.0)*${r0}
@ -6,50 +6,50 @@ variable d3 equal 3.0*${r0}
variable ro equal 2./${d1}/${d2}/${d3}
variable T equal 0.23
variable LD equal 1.0
variable LD equal 1.0
units lj
units lj
atom_style ellipsoid
boundary p p p
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 &
a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
region box block 0 40 0 24 -20 20
region box block 0 40 0 24 -20 20
create_box 1 box
region membrane block 0 40 0 24 -0.5 0.5
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
group membrane region membrane
set type 1 mass 1.0
set type 1 mass 1.0
set type 1 shape 1 1 1
set group all quat 0 -1 0 90
set group all quat 0 -1 0 90
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
thermo 200
timestep 0.01
dump 1 all atom 10 dump_onlymembrane.lammpstrj
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 2 all nve/asphere
fix 2 all nve/asphere
run 3000

100
examples/ASPHERE/flat_membrane/log.lammps → examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.1
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@ -1,6 +1,6 @@
LAMMPS (29 Sep 2021 - Update 3)
# only membrane
LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d1 equal 0.97
@ -16,7 +16,7 @@ variable ro equal 2./0.97/1.68008928334181/2.91
variable T equal 0.23
variable LD equal 1.0
units lj
units lj
atom_style ellipsoid
boundary p p p
@ -26,23 +26,23 @@ lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
Lattice spacing in x,y,z = 0.97000000 1.6800893 2.9100000
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
region box block 0 40 0 24 -20 20
region box block 0 40 0 24 -20 20
create_box 1 box
Created orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
1 by 1 by 1 MPI processor grid
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
using lattice units in orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
create_atoms CPU = 0.000 seconds
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
create_atoms CPU = 0.001 seconds
group membrane region membrane
1920 atoms in group membrane
set type 1 mass 1.0
set type 1 mass 1.0
Setting atom values ...
1920 settings made for mass
@ -50,12 +50,12 @@ set type 1 shape 1 1 1
Setting atom values ...
1920 settings made for shape
set group all quat 0 -1 0 90
set group all quat 0 -1 0 90
Setting atom values ...
1920 settings made for quat
compute memb all temp/com
compute rot all temp/asphere bias memb
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
velocity all create 0.23 87287 loop geom
@ -65,11 +65,11 @@ neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
thermo 200
timestep 0.01
dump 1 all atom 10 dump_onlymembrane.lammpstrj
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.23 ${T} ${LD} 48279
@ -77,7 +77,7 @@ fix 1 all langevin 0.23 0.23 ${LD} 48279
fix 1 all langevin 0.23 0.23 1 48279
fix 2 all nve/asphere
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
@ -97,8 +97,9 @@ Your simulation uses code contributions which should be cited:
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
@ -109,44 +110,44 @@ Neighbor list info ...
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.097 | 6.097 | 6.097 Mbytes
Step Temp Press Pxx Pyy
0 0.23 -0.0073508785 -0.012283389 -0.012234574
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
Loop time of 5.08921 on 1 procs for 3000 steps with 1920 atoms
Per MPI rank memory allocation (min/avg/max) = 5.024 | 5.024 | 5.024 Mbytes
Step Temp Press Pxx Pyy
0 0.23 -0.0073508785 -0.012283389 -0.012234574
200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
Loop time of 6.76659 on 1 procs for 3000 steps with 1920 atoms
Performance: 509312.653 tau/day, 589.482 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 383058.431 tau/day, 443.355 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2251 | 4.2251 | 4.2251 | 0.0 | 83.02
Neigh | 0.07599 | 0.07599 | 0.07599 | 0.0 | 1.49
Comm | 0.026195 | 0.026195 | 0.026195 | 0.0 | 0.51
Output | 0.21176 | 0.21176 | 0.21176 | 0.0 | 4.16
Modify | 0.53849 | 0.53849 | 0.53849 | 0.0 | 10.58
Other | | 0.01168 | | | 0.23
Pair | 5.7968 | 5.7968 | 5.7968 | 0.0 | 85.67
Neigh | 0.086077 | 0.086077 | 0.086077 | 0.0 | 1.27
Comm | 0.034761 | 0.034761 | 0.034761 | 0.0 | 0.51
Output | 0.00038014 | 0.00038014 | 0.00038014 | 0.0 | 0.01
Modify | 0.8268 | 0.8268 | 0.8268 | 0.0 | 12.22
Other | | 0.02181 | | | 0.32
Nlocal: 1920.00 ave 1920 max 1920 min
Nlocal: 1920 ave 1920 max 1920 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 772.000 ave 772 max 772 min
Nghost: 772 ave 772 max 772 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46804.0 ave 46804 max 46804 min
Neighs: 46804 ave 46804 max 46804 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46804
@ -155,7 +156,4 @@ Neighbor list builds = 99
Dangerous builds = 0
# notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem.
# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
# notes-3: pressure reach equilibrium much quicker than temperature
Total wall time: 0:00:05
Total wall time: 0:00:06

159
examples/ASPHERE/flat_membrane/log.18Oct22.flat_membrane.g++.4 Normal file
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@ -0,0 +1,159 @@
LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# flat membrane demo
variable r0 equal 0.97
variable d1 equal ${r0}
variable d1 equal 0.97
variable d2 equal sqrt(3.0)*${r0}
variable d2 equal sqrt(3.0)*0.97
variable d3 equal 3.0*${r0}
variable d3 equal 3.0*0.97
variable ro equal 2./${d1}/${d2}/${d3}
variable ro equal 2./0.97/${d2}/${d3}
variable ro equal 2./0.97/1.68008928334181/${d3}
variable ro equal 2./0.97/1.68008928334181/2.91
variable T equal 0.23
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
Lattice spacing in x,y,z = 0.97 1.6800893 2.91
region box block 0 40 0 24 -20 20
create_box 1 box
Created orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
1 by 1 by 4 MPI processor grid
region membrane block 0 40 0 24 -0.5 0.5
create_atoms 1 region membrane
Created 1920 atoms
using lattice units in orthogonal box = (0 0 -58.2) to (38.8 40.322143 58.2)
create_atoms CPU = 0.001 seconds
group membrane region membrane
1920 atoms in group membrane
set type 1 mass 1.0
Setting atom values ...
1920 settings made for mass
set type 1 shape 1 1 1
Setting atom values ...
1920 settings made for shape
set group all quat 0 -1 0 90
Setting atom values ...
1920 settings made for quat
#compute memb all temp/com
#compute rot all temp/asphere bias memb
velocity all create ${T} 87287 loop geom
velocity all create 0.23 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.01
#dump 1 all atom 10 dump_onlymembrane.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.23 ${T} ${LD} 48279
fix 1 all langevin 0.23 0.23 ${LD} 48279
fix 1 all langevin 0.23 0.23 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 22 23 65
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.794 | 5.472 Mbytes
Step Temp Press Pxx Pyy
0 0.23 -0.0073508785 -0.012283389 -0.012234574
200 0.20647718 -0.0012368074 -0.0021167303 -0.0015343502
400 0.21648371 -0.00085695085 -0.0015627331 -0.0011177093
600 0.22929515 -0.00050218657 -0.0008332 -0.00062622609
800 0.22062664 -0.00049172378 -0.000611884 -0.00075089294
1000 0.22422425 -0.00039405068 -0.00037600355 -0.00070786572
1200 0.2298767 -0.00025939082 -0.00021616578 -0.00053125505
1400 0.2335927 5.8028332e-05 0.00017530192 -3.1675138e-05
1600 0.22884878 -0.0001733902 -0.0008056431 0.00014276754
1800 0.22813498 0.00019873459 0.00051040124 5.8860949e-05
2000 0.2273166 -3.3595127e-05 0.0001705632 -0.00026498213
2200 0.2251643 -2.4517311e-05 -4.0618888e-05 1.066658e-05
2400 0.22460629 -4.5661259e-05 -0.00019144039 -1.6649099e-05
2600 0.23085675 0.00014029405 0.00017983536 0.00017895001
2800 0.22364591 4.2999164e-05 -0.00011000466 0.00024363243
3000 0.23421357 0.00023505702 0.00020752013 0.00053567111
Loop time of 4.68577 on 4 procs for 3000 steps with 1920 atoms
Performance: 553164.568 tau/day, 640.237 timesteps/s
95.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00015072 | 1.6029 | 3.8573 | 131.7 | 34.21
Neigh | 0.00055747 | 0.025423 | 0.065858 | 17.0 | 0.54
Comm | 0.0052259 | 0.48173 | 1.624 | 96.5 | 10.28
Output | 0.0003894 | 0.023428 | 0.047223 | 15.0 | 0.50
Modify | 0.00037337 | 0.2141 | 0.44595 | 46.3 | 4.57
Other | | 2.338 | | | 49.90
Nlocal: 480 ave 1011 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 860 ave 1771 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 11697.8 ave 30095 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Total # of neighbors = 46791
Ave neighs/atom = 24.370313
Neighbor list builds = 99
Dangerous builds = 0
Total wall time: 0:00:04

18
examples/ASPHERE/vesicle/in.vesicle
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@ -1,9 +1,9 @@
# Vesicle demo
# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
variable LD equal 1.0
units lj
units lj
atom_style ellipsoid
boundary p p p
@ -16,20 +16,18 @@ compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
thermo 200
timestep 0.001
dump 1 all atom 10 onlymembrane2.lammpstrj
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 2 all nve/asphere
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 2 all nve/asphere
run 3000

122
examples/ASPHERE/vesicle/log.18Oct22.vesicle.g++.1 Normal file
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@ -0,0 +1,122 @@
LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
Reading data file ...
orthogonal box = (-35 -35 -35) to (35 35 35)
1 by 1 by 1 MPI processor grid
reading atoms ...
2938 atoms
2938 ellipsoids
read_data CPU = 0.010 seconds
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
velocity all create 0.2 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.2 ${T} ${LD} 48279
fix 1 all langevin 0.2 0.2 ${LD} 48279
fix 1 all langevin 0.2 0.2 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 39 39 39
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.091 | 5.091 | 5.091 Mbytes
Step Temp Press Pxx Pyy
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
Loop time of 9.6866 on 1 procs for 3000 steps with 2938 atoms
Performance: 26758.610 tau/day, 309.706 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 8.3097 | 8.3097 | 8.3097 | 0.0 | 85.79
Neigh | 0.039037 | 0.039037 | 0.039037 | 0.0 | 0.40
Comm | 0.0021766 | 0.0021766 | 0.0021766 | 0.0 | 0.02
Output | 0.00048628 | 0.00048628 | 0.00048628 | 0.0 | 0.01
Modify | 1.3043 | 1.3043 | 1.3043 | 0.0 | 13.47
Other | | 0.0309 | | | 0.32
Nlocal: 2938 ave 2938 max 2938 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73242 ave 73242 max 73242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 73242
Ave neighs/atom = 24.929204
Neighbor list builds = 26
Dangerous builds = 0
Total wall time: 0:00:09

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LAMMPS (15 Sep 2022)
using 1 OpenMP thread(s) per MPI task
# Vesicle demo
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
Reading data file ...
orthogonal box = (-35 -35 -35) to (35 35 35)
1 by 2 by 2 MPI processor grid
reading atoms ...
2938 atoms
2938 ellipsoids
read_data CPU = 0.137 seconds
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
velocity all create 0.2 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
#dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.2 ${T} ${LD} 48279
fix 1 all langevin 0.2 0.2 ${LD} 48279
fix 1 all langevin 0.2 0.2 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update: every = 1 steps, delay = 10 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 39 39 39
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.899 | 4.9 | 4.902 Mbytes
Step Temp Press Pxx Pyy
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
200 0.12893798 -0.0051492794 -0.0048734875 -0.0049624005
400 0.13798694 -0.004875313 -0.0047071897 -0.0049305051
600 0.14725193 -0.0046349542 -0.004719983 -0.0045791451
800 0.16146954 -0.0042232199 -0.0040789193 -0.0043672895
1000 0.17268468 -0.0037146703 -0.0036270393 -0.0039169034
1200 0.18266242 -0.0032749755 -0.0032971704 -0.0033323855
1400 0.18500165 -0.0028179031 -0.0030659821 -0.0027519633
1600 0.19513132 -0.0023407512 -0.0025109801 -0.0023416835
1800 0.19645259 -0.0019995412 -0.0019064341 -0.0021757747
2000 0.19658104 -0.0015897919 -0.0015850523 -0.0016828478
2200 0.1989936 -0.0011794062 -0.0011779716 -0.0012070706
2400 0.20011525 -0.0009147432 -0.00094040885 -0.001073922
2600 0.2013975 -0.00059253676 -0.00051920304 -0.00075138934
2800 0.19715513 -0.00020995605 -0.00024386426 -0.0005475745
3000 0.1976782 -0.0001308553 5.693004e-05 -0.00034478469
Loop time of 8.46954 on 4 procs for 3000 steps with 2938 atoms
Performance: 30603.800 tau/day, 354.211 timesteps/s
77.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1751 | 2.4162 | 2.6707 | 13.2 | 28.53
Neigh | 0.0090503 | 0.0098389 | 0.010503 | 0.6 | 0.12
Comm | 3.5807 | 4.1526 | 4.9283 | 24.3 | 49.03
Output | 0.00032165 | 0.0029648 | 0.010842 | 8.4 | 0.04
Modify | 0.34554 | 0.37442 | 0.39198 | 2.8 | 4.42
Other | | 1.514 | | | 17.87
Nlocal: 734.5 ave 739 max 730 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Nghost: 420.25 ave 424 max 415 min
Histogram: 1 0 0 0 0 1 0 1 0 1
Neighs: 18304.5 ave 19839 max 16636 min
Histogram: 1 0 0 0 1 0 1 0 0 1
Total # of neighbors = 73218
Ave neighs/atom = 24.921035
Neighbor list builds = 25
Dangerous builds = 0
Total wall time: 0:00:08

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LAMMPS (29 Sep 2021 - Update 3)
variable T equal 0.2
variable LD equal 1.0
units lj
atom_style ellipsoid
boundary p p p
read_data read_data.vesicle1026
Reading data file ...
orthogonal box = (-35.000000 -35.000000 -35.000000) to (35.000000 35.000000 35.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
2938 atoms
2938 ellipsoids
read_data CPU = 0.008 seconds
compute ali all temp/com
compute rott all temp/asphere bias ali
velocity all create ${T} 87287 loop geom
velocity all create 0.2 87287 loop geom
pair_style ylz 2.6
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
neighbor 1.0 bin
thermo_style custom step temp press pxx pyy
thermo 200
timestep 0.001
dump 1 all atom 10 onlymembrane2.lammpstrj
fix 1 all langevin ${T} ${T} ${LD} 48279
fix 1 all langevin 0.2 ${T} ${LD} 48279
fix 1 all langevin 0.2 0.2 ${LD} 48279
fix 1 all langevin 0.2 0.2 1 48279
fix 2 all nve/asphere
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair ylz command:
@Article{Yuan10,
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
journal = {Phys. Rev. E},
year = 2010,
volume = 82,
pages = {011905}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 3.6
ghost atom cutoff = 3.6
binsize = 1.8, bins = 39 39 39
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair ylz, perpetual
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes
Step Temp Press Pxx Pyy
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
Loop time of 7.2222 on 1 procs for 3000 steps with 2938 atoms
Performance: 35889.329 tau/day, 415.386 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.0158 | 6.0158 | 6.0158 | 0.0 | 83.30
Neigh | 0.034308 | 0.034308 | 0.034308 | 0.0 | 0.48
Comm | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.02
Output | 0.31567 | 0.31567 | 0.31567 | 0.0 | 4.37
Modify | 0.83787 | 0.83787 | 0.83787 | 0.0 | 11.60
Other | | 0.01702 | | | 0.24
Nlocal: 2938.00 ave 2938 max 2938 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73242.0 ave 73242 max 73242 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 73242
Ave neighs/atom = 24.929204
Neighbor list builds = 26
Dangerous builds = 0
# notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem.
# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
# notes-3: pressure reach equilibrium much quicker than temperature
Total wall time: 0:00:07